.callHarman

callHarman

2D NumericMatrix of PCA scores data (from the
<code>prcomp$x</code> slot), rows = samples, cols = PC scores

pc_data_scores

The structure of the experiment, consisting of batch numbers and
treatment numbers forming 2 rows or columns (HarmanMain works out which).
Each entry for a sample describes what batch it came from and what treatment
it was given. Has to be integer formated data.

group

A double precsion value indicating the limit of confidence in
which to stop removing a batch effect

limit

The number of repeats in which to run the simulated batch
mean distribution estimator. Probably should be greater than 100,000.

numrepeats

Random seed to pass to the random number generator (0 for use
default from system time)

randseed

forceRand

printInfo


This wrapper should probably not be addressed directly except
for debugging. Instead use <code><a rd-options="" href="/link/harman?package=Harman&version=1.0.2" data-mini-rdoc="Harman::harman">harman</a></code>. Input of PCA scores and the
experiment structure (treatments and batches) and returns a batch corrected
version of the PCA scores matrix


Harman is a PCA and constrained optimisation based
technique that maximises the removal of batch effects from
datasets, with the constraint that the probability of
overcorrection (i.e. removing genuine biological signal along
with batch noise) is kept to a fraction which is set by the
end-user.

Jason Ross

Harman

The removal of batch effects from datasets using a PCA and
constrained optimisation based technique

callHarman function

This wrapper should probably not be addressed directly except
for debugging. Instead use <code><a href="harman" rd-options="">harman</a></code>. Input of PCA scores and the
experiment structure (treatments and batches) and returns a batch corrected
version of the PCA scores matrix

callHarman: Wrapper function to call the shared C/C++ library code

Description

Usage

Arguments

Value